Special conditions are required for genetic differentiation to arise at a small geographical scale and in the face of gene flow.The Natal multimammate mouse,Mastomys natalensis,is the most widely distributed and abundant rodent in Sub-Saharan Africa.A notorious agricultural pest and a natural host for many zoonotic diseases,it can live in close proximity to man,and appears to compete with other rodents for the synanthropic niche.We surveyed its population genetic structure across a 180 km transect in central Tanzania along which the landscape varied between agricultural land in a rural setting and natural woody vegetation,rivers,roads and a city.We sampled M.natalensis across 10 localities,and genotyped 15 microsatellite loci from 515 individuals.Minimising genetic disequilibria,hierarchical STRUCTURE analyses show a K-invariant pattern distinguishing Morogoro city (located in the centre of the transect) from 9 surrounding rural localities.Neither geographical isolation (through landscape analyses in Circuitscape) nor natural breeding asynchrony (through comparison of rainfall patterns) could explain the genetic differentiation of the urban population.Using the Isolation-with-Migration model implemented in IMa2 we inferred that a split between suburban and rural populations would have occurred recently (<150 years ago) with higher urban effective population density consistent with an urban source to rural sink of effective migration.The observed genetic differentiation of urban multimammate mice is striking given the uninterrupted distribution of the animal throughout the landscape and the high estimates of effective migration (2NeM = 3.0 and 29.7) ,suggesting a strong selection gradient across the urban boundary.